Nickel in PDB 5c3s: Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU)

The structure of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU), PDB code: 5c3s was solved by W.Li, T.Zhang, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.801, 155.604, 75.954, 90.00, 91.74, 90.00
R / Rfree (%)	18.4 / 22.8

The binding sites of Nickel atom in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU) (pdb code 5c3s). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU), PDB code: 5c3s:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:18.7 occ:1.00 O1 A:AKG402 2.1 20.3 1.0 O5 A:AKG402 2.2 20.9 1.0 OD1 A:ASP216 2.2 14.9 1.0 NE2 A:HIS271 2.2 13.1 1.0 O A:HOH501 2.2 14.1 1.0 NE2 A:HIS214 2.3 15.4 1.0 C1 A:AKG402 2.8 20.0 1.0 C2 A:AKG402 2.9 20.9 1.0 CG A:ASP216 3.0 15.4 1.0 CD2 A:HIS271 3.1 12.9 1.0 OD2 A:ASP216 3.1 15.8 1.0 CE1 A:HIS214 3.2 14.9 1.0 CD2 A:HIS214 3.2 14.9 1.0 CE1 A:HIS271 3.3 13.2 1.0 O2 A:AKG402 4.1 19.2 1.0 O A:HOH657 4.1 34.2 1.0 O3 A:FYU403 4.1 33.4 1.0 CG A:HIS271 4.3 13.2 1.0 ND1 A:HIS214 4.3 15.3 1.0 ND1 A:HIS271 4.3 13.3 1.0 C3 A:AKG402 4.3 20.6 1.0 CG A:HIS214 4.4 15.1 1.0 CB A:ASP216 4.5 15.1 1.0 CE1 A:PHE292 4.5 14.4 1.0 CM5 A:FYU403 4.7 30.9 1.0 C4 A:AKG402 4.8 21.1 1.0 N A:ASP216 4.9 14.8 1.0 CA A:ASP216 4.9 15.0 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:24.2 occ:1.00 O2 B:AKG402 2.1 27.8 1.0 NE2 B:HIS271 2.2 18.4 1.0 O B:HOH540 2.2 22.4 1.0 OD1 B:ASP216 2.3 20.7 1.0 NE2 B:HIS214 2.3 19.2 1.0 O5 B:AKG402 2.3 28.1 1.0 C1 B:AKG402 2.9 28.4 1.0 C2 B:AKG402 2.9 27.8 1.0 CE1 B:HIS271 3.1 18.3 1.0 CG B:ASP216 3.1 20.9 1.0 CD2 B:HIS271 3.2 18.4 1.0 CD2 B:HIS214 3.2 19.6 1.0 CE1 B:HIS214 3.3 19.3 1.0 OD2 B:ASP216 3.3 21.9 1.0 O1 B:AKG402 4.1 28.2 1.0 O B:HOH628 4.1 36.7 1.0 O3 B:FYU404 4.2 34.7 1.0 ND1 B:HIS271 4.2 18.3 1.0 CG B:HIS271 4.3 18.2 1.0 ND1 B:HIS214 4.4 19.9 1.0 CG B:HIS214 4.4 19.8 1.0 C3 B:AKG402 4.4 26.6 1.0 CE1 B:PHE292 4.5 21.4 1.0 CB B:ASP216 4.5 20.6 1.0 CM5 B:FYU404 4.6 32.9 1.0 N B:ASP216 4.9 20.3 1.0 CA B:ASP216 4.9 20.7 1.0 C4 B:AKG402 4.9 25.6 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:21.7 occ:1.00 O2 C:AKG402 2.2 23.7 1.0 O5 C:AKG402 2.2 22.9 1.0 NE2 C:HIS271 2.2 14.9 1.0 NE2 C:HIS214 2.2 18.0 1.0 O C:HOH505 2.3 18.2 1.0 OD1 C:ASP216 2.3 17.6 1.0 C2 C:AKG402 2.9 23.6 1.0 C1 C:AKG402 2.9 23.8 1.0 CG C:ASP216 3.1 17.9 1.0 CE1 C:HIS271 3.1 14.7 1.0 CD2 C:HIS214 3.2 18.2 1.0 CD2 C:HIS271 3.2 14.9 1.0 CE1 C:HIS214 3.2 18.2 1.0 OD2 C:ASP216 3.2 17.8 1.0 O C:HOH615 4.0 35.8 1.0 O1 C:AKG402 4.1 24.2 1.0 ND1 C:HIS271 4.2 14.6 1.0 ND1 C:HIS214 4.3 18.6 1.0 CG C:HIS271 4.3 14.8 1.0 CG C:HIS214 4.3 18.6 1.0 C3 C:AKG402 4.3 23.4 1.0 CM5 C:FYU404 4.4 37.4 1.0 CB C:ASP216 4.5 17.7 1.0 CE1 C:PHE292 4.5 23.8 1.0 O3 C:FYU404 4.6 40.0 1.0 C4 C:AKG402 4.8 23.2 1.0 N C:ASP216 4.9 17.7 1.0 CZ C:PHE292 4.9 24.2 1.0 CA C:ASP216 4.9 17.8 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Formyluracil (5FU) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:26.9 occ:1.00 O5 D:AKG402 2.1 32.8 1.0 O1 D:AKG402 2.2 32.3 1.0 NE2 D:HIS214 2.2 22.9 1.0 OD1 D:ASP216 2.2 24.8 1.0 NE2 D:HIS271 2.3 20.7 1.0 O D:HOH508 2.3 24.7 1.0 C2 D:AKG402 2.8 33.9 1.0 C1 D:AKG402 2.8 33.2 1.0 CE1 D:HIS214 3.1 23.2 1.0 CG D:ASP216 3.1 24.2 1.0 CD2 D:HIS271 3.2 20.4 1.0 OD2 D:ASP216 3.2 23.9 1.0 CE1 D:HIS271 3.2 20.5 1.0 CD2 D:HIS214 3.2 23.2 1.0 O2 D:AKG402 4.1 32.9 1.0 ND1 D:HIS214 4.2 23.3 1.0 C3 D:AKG402 4.3 33.7 1.0 ND1 D:HIS271 4.3 20.9 1.0 CG D:HIS271 4.3 20.6 1.0 CG D:HIS214 4.3 23.2 1.0 O3 D:FYU404 4.4 50.5 1.0 CB D:ASP216 4.5 23.5 1.0 CE1 D:PHE292 4.6 25.9 1.0 C4 D:AKG402 4.7 34.3 1.0 CM5 D:FYU404 4.9 50.7 1.0 N D:ASP216 5.0 22.7 1.0 CA D:ASP216 5.0 23.4 1.0

W.Li, T.Zhang, J.Ding. Molecular Basis For the Substrate Specificity and Catalytic Mechanism of Thymine-7-Hydroxylase in Fungi Nucleic Acids Res. V. 43 10026 2015.
ISSN: ESSN 1362-4962
PubMed: 26429971
DOI: 10.1093/NAR/GKV979